MolNFT v1 · #120697 · protein
Crystal structure of medicago truncatula N-carbamoylputrescine amidohydrolase (mtcpa) in complex with cadaverine
5H8J: “Crystal structure of medicago truncatula N-carbamoylputrescine amidohydrolase (mtcpa) in complex with…”. X-ray diffraction, 1 ligand (N2P), 20 pockets (best druggability 0.83). MolNFT v1 #120697 on GenesisL1: 3D structure, binding…
- PDB
- 5H8J
- Type
- protein
- Length
- 4,712 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-carbamoylputrescine amidohydrolase
- UniProt
- G7ITU5
- Ligands
- N2P
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-carbamoylputrescine amidohydrolase | protein | 296 | 30% helix, 29% strand | G7ITU5 |
| B, E | N-carbamoylputrescine amidohydrolase | protein | 297 | 31% helix, 30% strand | G7ITU5 |
| C, K | N-carbamoylputrescine amidohydrolase | protein | 301 | 30% helix, 30% strand | G7ITU5 |
| D, F, J, L, M, N, O | N-carbamoylputrescine amidohydrolase | protein | 298 | 31% helix, 30% strand | G7ITU5 |
| G | N-carbamoylputrescine amidohydrolase | protein | 295 | 29% helix, 31% strand | G7ITU5 |
| H | N-carbamoylputrescine amidohydrolase | protein | 268 | 31% helix, 24% strand | G7ITU5 |
| I | N-carbamoylputrescine amidohydrolase | protein | 292 | 31% helix, 30% strand | G7ITU5 |
| P | N-carbamoylputrescine amidohydrolase | protein | 279 | 30% helix, 29% strand | G7ITU5 |
Ligands and binding sites
- N2P · Pentane-1,5-diamine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- GOL · Glycerol · additive · 25 copies · chains A, B, C, D, E, F, G, L, H, I, J, K, M, N, O, P
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D, E, F, I, J, K, L, M, N
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains G, L
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.83 | 0.97 | 36 | empty |
| 2 | 204 | 0.83 | 0.97 | 37 | EDO |
| 3 | 192 | 0.83 | 0.97 | 38 | EDO |
| 4 | 192 | 0.83 | 0.97 | 38 | empty |
| 5 | 202 | 0.82 | 0.96 | 37 | EDO |
Interfaces
33 interfaces between chains.
- M–N · 2507 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2493 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2484 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 2477 Ų buried · 37 hydrogen bonds · protein-protein
- I–J · 2431 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5H8J · Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt G7ITU5
- Elsewhere: RCSB PDB 5H8J · PDBe 5H8J · UniProt G7ITU5
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